<p>With the development of the shipping industry, the pollution problem caused by vessel fuels is becoming increasingly severe. Due to the great mobility and on-demand service capability of Unmanned Aerial Vehicles (UAVs), UAVs have become effective tools for detecting pollution in Emission Control Areas (ECAs). How to obtain the effective trajectories of UAVs within the energy limitation and the time limitation is a difficult problem to solve. The paper investigates the trajectory planning problem in UAV-assisted vessel emission detection system. In the problem, the sailing vessels in a given area are taken as the detection tasks and multiple UAVs are ready to detect these vessels. Each vessel is assigned a different detecting weight and sails to the port at a different speed. The objective is to complete as many detection tasks as possible before the deadline and maximize the total weight of these completed tasks. A Genetic Algorithm (GA)-based trajectory planning algorithm framework is proposed for the problem under study. The framework consists of key components, such as the chromosome generation method to generate chromosomes of each generation, the feasible solution generation method to compute the feasible solution according to the sequence defined in a chromosome, and the chromosome reconstruction method to improve the quality of chromosomes based on history information. The experimental results show that the proposed algorithm outperforms the baseline algorithms in terms of effectiveness and robustness.</p>